Thursday, January 22, 2009

Darwin Was Wrong?

The cover is this week's issue of New Scientist is sure to get your attention.

I happen to believe that the science of evolutionary biology has moved on since 1859, and I happen to be a proponent of evolutionary processes that Darwin new nothing about. Nevertheless, proclaiming that "Darwin was wrong" is a different story. That's an egregious example of journalistic hype and it's unacceptable in a magazine like New Scientist.

The essence of the story is that the early history of evolution is probably characterized by a net of life and not a traditional tree. The "net" metaphor is due to many example of lateral gene transfer.

Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth. At its base is LUCA, the Last Universal Common Ancestor of all living things, and out of LUCA grows a trunk, which splits again and again to create a vast, bifurcating tree. Each branch represents a single species; branching points are where one species becomes two. Most branches eventually come to a dead end as species go extinct, but some reach right to the top - these are living species. The tree is thus a record of how every species that ever lived is related to all others right back to the origin of life.

For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree. "For a long time the holy grail was to build a tree of life," says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.

As it happens, I was at a function last night with Jan Sapp of York University (Toronto, Canada). Loyal Sandwalk readers might recall a series of articles on the Three Domain Hypothesis. The articles were based on a book edited by Jan Sapp. Sapp is a supporter, as am I, of the scheme advocated by Ford Doolittle (see below).

This net, or web, of life is characteristic of the earliest stages of evolution when all organisms were single cells and the distinction between eukaryotes and prokaryotes was barely discernible. Once the main groups rose out of the web, they evolved pretty much as you light expect by binary speciation events. This gives rise to a traditional tree-like pattern.

As Jan and I discussed, for the last three billion years of evolution the tree of life is a very good metaphor for evolution. Darwin was mostly right about that. On the other hand, the New Scientist article discusses some problems with the tree of life that extend beyond the early history. It makes several valid points that should make everyone skeptical of claims about evolution that are too simple. The tree isn't perfect.

The bottom line is that it's unfair to say that Darwin was wrong. It's as unfair as saying the Newton was wrong because of Einstein. We need to recognize that modern evolutionary biology is an improvement over the view of the Victorian founder of the field, but a cover saying that Darwin was wrong conveys the wrong message. It suggests that up until recently scientists believed that Darwin was right about everything.

A better headline might be: "More evidence that Charles Darwin didn't know everything there is to be known about evolution when he published his book in 1859."

UPDATE: In a surprising development, the IDiots at Uncommon Descent have picked up on these recent (sic) developments in evolutionary theory. Paul Nelson, a Young Earth Creationist philosopher, writes: “The tree of life is being politely buried”.

50 comments
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So, is the title an outright media ploy - pandering for profit – or, does Lawton lack some fundamental understanding of scientific progress? Either way, I would have expected more from New Scientist. I wonder if there’s an editor catching heat over somewhere…

Wait a minute guys, there's something going on here, because, look what Dr.Craig Venter said "The tree of life is an artifact of some early scientific studies that aren't really holding up…So there is not a tree of life." a this guy is no scientific know nothing!

The essence of the story is that the early history of evolution is probably characterized by a net of life and not a traditional tree. The "net" metaphor is due to many example of lateral gene transfer.

Lateral gene transfer depends upon a shared genetic code. A shared genetic code is evidence of a common origin. The "net" approach is not a rejection of a common origin, but a rejection of the notion that the branches of the "tree" have always divided and never merged.

Sheesh. How totally irresponsible. Create an inflammatory cover to generate a false controversy and sell magazines... and in the process, give the IDers one more piece of fuel for their bonfire of stupidity. Nice work, guys.

You know it's more due to the fact that the genes are only often kept in check by being completely contained within certain specific species that this "revelation" comes even remotely close to a revelation.

Rather than tracking the origins of organisms we should be properly looking at what must necessarily be a tree due to the nature of evolution: The tree of genes. We simply aren't there yet, but we're getting closer.

There is still something crucial missing in the net of life. When will the lowly virus get the respect it deserves? I realize that many biologists don't even consider viruses to be "alive", but if we're talking about origins and the where and how of the distribution of genetic material, they cannot just be ignored.

The ID/creationists can be expected to run with this magazine story, quote-mine it, and otherwise play their games. But sadly for them, it does nothing to advance their ideology because what they're peddling still isn't true.

My thoughts, here:http://rhinocrisy.org/2009/01/darwin-was-a-long-time-ago/including the money quote from Doolittle on creationists:"... [The tree of life] should not be an essential element in our struggle against those who doubt the validity of evolutionary theory, who can take comfort from this challenge to the TOL only by a willful misunderstanding of its import."

What's amazing to me is how much Darwin got right, based on what was known at the time. For example, he knew nothing of genes or genetics. The great thing is that Mendel knew nothing of Darwin either, yet you take the work of each, put it together and it fits perfectly. To me, this is great evidence that something is "right" or describes something "real" - two bodies of work, unconnected, unaware of each other, yet perfectly complementary.

Whatever you think of the overall picture about the "tree of life" today, I think it's only fair to judge Darwin's work for what he actually studied, with the knowledge of his day. (As I would like to think that historians do, but then I'm not an historian!)

It seems to me that there are broadly two classes of things that Darwin didn't know about (and more-or-less could not have known about) that are involved: detailed studies of the evolution of bacteria, fungi and viruses; and the lower-level molecular mechanisms of genetics.

For the species Darwin did examine, limited to the mechanisms he was able to study, the tree of life concept was fine and largely still is. It's just more knowledge on other species and lower-level mechanisms has elaborated the concept since his time.

Doolittle's work is (was?), as ever, wonderful. I remember reading his earlier papers as a kid, teaching myself "bioinformatics" in the evening at the university library (there were no bioinformatics courses at the time).

As for the title on the cover, can you say someone was wrong about something that they were not referring to or could not know about?

Graham Lawton here.A gentle plea: please read the article before shooting off about it. Judging from these comments most of you haven't bothered. That is "totally unnaceptable" (to use a phrase Larry is fond of when lecturing journalists).

I'm happy to have a reasonable discussion of the ideas in the feature, once you've all stopped flying off the handle about the cover line of the magazine (not the headline of the article, or the article itself) and what you assume I wrote.

Oh, and Johnny: sorry to disillusion you but I've got a pretty good understanding of scientific progress. You, however, lack a fundamental understanding of how the media works.

You, however, lack a fundamental understanding of how the media works.

Enlighten, please. No, really. I actually am interested in which bits you feel responsible for, and which were out of your control, and *how* you feel about those bits out of your control (e.g., the cover, presumably).

The way we work here is that the writer of the piece generally has almost no say over the headline, standfirst and other bits of "page furniture". These are the resonsibility of the copy editor and the sub-editors. The online version often has its own headline, which again is out of the control of the writer (in this case the magazine headline is "Uprooting Darwin's Tree").

Coverlines, similarly, are written not by the writer but by senior editors with the express purpose of selling the magazine (the line between marketing and journalism blurs a little here).

As I'm a senior editor too, however, I can't and won't claim that the coverline was entirely beyond my control. Not my ultimate decision, but I was in on the discussions. We knew we were courting controversy but the feeling was that the story was solid enough to allow us to be provocative and, in any case, the statement is true.

So I feel very strong ownership of the article itself, particularly the print version (and I totally stand by the story, which is the product of weeks of hard work, extensive interviews with scientists, a stack of journal papers and much thought, despite what some bloggers are saying). I feel some ownership of the front cover "sell", though as always I'm acutely aware that it is 50% journalism, 50% sales pitch.

Do you think reporting this absurd blanket statement as fact is responsible journalism? Your article goes on to provide some degree of qualification (e.g. "While vertical descent is no longer the only game in town, it is still the best way of explaining how multicellular organisms are related to one another - a tree of 51 per cent, maybe."). However, were I writing the piece, I'd be immediately pulling up Bapteste on his idiotic and thoroughly unhelpful hyperbole.

"A gentle plea: please read the article before shooting off about it."

We don't need to read the article to criticize the cover page. We've long known that Darwin was wrong about a great many things. Turning it into front page news 150 years after the fact makes it seem like he was wrong about the *one* thing that really matters.

"We knew we were courting controversy but the feeling was that the story was solid enough to allow us to be provocative and, in any case, the statement is true... as always I'm acutely aware that it is 50% journalism, 50% sales pitch."

UPDATE: In a surprising development, the IDiots at Uncommon Descent have picked up on these recent (sic) developments in evolutionary theory. Paul Nelson, a Young Earth Creationist philosopher, writes: “The tree of life is being politely buried”.

Quoting somebody isn't tantamount to endorsing their views. It's about reporting what experts are thinking and getting their views on record. It shows that you're not just making stuff up, but reporting something that is really going on.

People here are ABSOLUTELY justified in judging this by the cover alone; that's EXACTLY what the creationists are doing, and that's why we're reacting. Notice that your work is now popping up across the IDiot blogosphere.

If you had even a semblance of a clue, you'd have known this was going to happen, and that the sensationalist headline would be acting against your magazine's ostensible purpose of informing people about science.

Bueller_007 said: Notice that your work is now popping up across the IDiot blogosphere.

If you had even a semblance of a clue, you'd have known this was going to happen,...

I notice in New Scientist's editorial on this article it says: "None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that "New Scientist has announced Darwin was wrong". Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not." It seems those idiots at New Scientsit do have a semblance of a clue.

My point was that creationists would not even read the article, but just delight in the headline. I have little doubt that the article itself is based more or less on sound science that would refute creationist claims.

The comment that you cite means very little to those who actually bother to read the article, and is hidden away from those who don't. In other words, it has no effect on those who don't.

A responsible cover would have included an excoriation of creationists.

re I'm happy to have a reasonable discussion of the ideas in the feature, once you've all stopped flying off the handle about the cover line of the magazine (not the headline of the article, or the article itself) and what you assume I wrote.

If this is what you want, could I suggest that you not paste everyone with the same brush? (You are also assuming that everyone has not read the article or at least got the gist of it.)

The headline used certainly can be misleading, you essentially admitted as much. In my opinion, if you are going to use a "racy" or "teasing" headline, the article is going to have to go out of its way to disclaim any misinterpretations of the headline. In this case, I am not convinced that has been done.

I don't think this style of headline is appropriate for a science magazine: it's usually used to try to create major controversy where the the reality is minor controversy or even none. The terms "media beat up" or "hype" come to mind. It has it's place in "entertainment" publications like the Sun (What, it carries real news?! Just kidding.)

There is a controversy of sorts, but it's more minor than the headline makes out and not really about if "Darwin was right" or not.

Turning to the science and the article itself, there are many points that you don't make clear enough to readers, I feel. I realise you can't cover it all one small article, but I think the focus on presenting examples of one process with little balance of the other mechanisms and issues isn't helpful. These add complexity to the story, but if you are going to raise this topic, you really can't avoid these I feel.

I'm going to toss out a few random examples to give some idea of what I mean. This aren't meant to be definitive (or even especially accurate), but rather to show considerations that might have been included that might lead to a more balanced presentation of the issue. (I've also stuck with simpler cases that might be easier to present to a general readership.)

More than just observing examples of HGT is needed to claim that these events are species-forming. This, in turn, brings up that a gene-based phylogenetic tree constructed from a limited number of genes may not necessarily be congruent with the "true" species tree.

As a hypothetical (counter-)example, if a small number of individuals acquire a gene via HGT, the population may "drift" to have this new gene present at a high frequency with no speciation event occur.

You need to make clearer to readers that in biology exceptions to the rule are expected (I usually like to cite Jacob François' famous line "evolution is a tinkerer" for this). Finding a group of organisms exhibiting high levels of HGT or specific examples won't count for a lot in terms of over-throwing a larger generalisation.

With that in mind, you don't present the frequency of speciation events due to HGT against speciation events not needing HGT, and for what lines of life in a way that I think a naïve reader might get a feel for the balance of the two. At worst, presenting a list examples where HGT has a role without balancing it with cases where it does not might lead a naïve reader to believe that HGT is the only mechanism for speciation for all forms of life!

On that note, your extrapolating from the examples you give for eukaryotes stretches your argument too far, in my opinion. Among other things, you make no mention that for "higher" eukaryotes, new genes must be incorporated into and passed on via the germ line, an issue not faced by single-celled life, which puts considerable limitations on acquiring new genes via HGT compared with single-cellular life.

Another thing you might have explored is if the mechanisms seen in eukaryotes are used in forming most species, or predominantly in higher-order groups.

In the case of bacteria in particular, you can even turn your argument completely on it's head and ask if it is the definition of "species" that needs revising, rather than the trees, a point you don't raise. That is, you could have considered if the traditional "species" notion is appropriate for single-celled life and viruses (nods to ERV ;-) ).

There are other science points, but that's me done for now :-) You have presented it as an argument for "knocking over" "the" tree of life, rather than elaborating it. This strikes me as a journalistic construct, "creating a conflict". Wording like "the battle over the tree", is pure journalism, of course, as are some other passages which read as hyperbole to me, e.g. "But today the project lies in tatters, torn to pieces by an onslaught of negative evidence." This isn't at all how it is perceived, at least to this scientist. In my experience scientists are more likely to say "Hmm. That's interesting".

Just a personal note to close this overly long ramble. A little while I ago I remarked to a friend that if I buy a magazine, it'd usually be NewScentist. She replied to the effect that she thought it to be sensationalist. I realised since then that I haven't actually bought a copy for some years (budgets and all that). Since then I have reconsidered my opinion of NewScientist. If I were to judge by the current headlines and hype, I probably wouldn't look at a lot of the issues. Just food for thought. You might want to consider that you are alienating some of your potential readership with headlines like that, and articles on "big" topics playing only or largely one side of an argument.

John Pieret points out that the New Scientist article has already apparently been cited by a creationist Board member in support of weakening the Texas science standards (see here for the original story:

Barbara Cargill, a Republican who supported the weaknesses requirement, said there have been “significant challenges” to the theory of evolution and she cited a recent news article in which a European scientist disputed Darwin’s “tree of life” showing common ancestors for all living things.

The New Scientist is probably trying to catch the attention of creationists and have new readers. My guess is that creationists will only read the cover and fill their blogs with completely nonsenses about the tree of life. That's not the way a scientific magazine should vulgarize science. Scientific American has chosen a different approach, their cover title is: The Evolution Of Evolution - How Darwin's theory survives, thrives and reshapes the world. I am "amazed" on how intense is the debate about evolution in the US. In Europe it's not even a subject of discussion. All my support and encouragement to all the Americans who defend science against superstitions.

In the high-stakes game of preserving sage grouse, biologists say they’re still figuring out how the birds will react to the influx of wind turbines rising up from the wide-open sagebrush plains where the birds evolved.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.